How To Install pal2nal on Ubuntu 22.04
Introduction
In this tutorial we learn how to install pal2nal on Ubuntu 22.04.
What is pal2nal
pal2nal is:
PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon-based DNA alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon-based DNA alignment can further be subjected to the calculation of synonymous (Ks) and non-synonymous (Ka) substitution rates.
There are three methods to install pal2nal on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install pal2nal Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pal2nal using apt-get by running the following command:
sudo apt-get -y install pal2nal
Install pal2nal Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pal2nal using apt by running the following command:
sudo apt -y install pal2nal
Install pal2nal Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install pal2nal using aptitude by running the following command:
sudo aptitude -y install pal2nal
How To Uninstall pal2nal on Ubuntu 22.04
To uninstall only the pal2nal package we can use the following command:
sudo apt-get remove pal2nal
Uninstall pal2nal And Its Dependencies
To uninstall pal2nal and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove pal2nal
Remove pal2nal Configurations and Data
To remove pal2nal configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge pal2nal
Remove pal2nal configuration, data, and all of its dependencies
We can use the following command to remove pal2nal configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pal2nal
References
Summary
In this tutorial we learn how to install pal2nal package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
